This might depend on how the motherboard initializes the USB subsystem.
Since a change of the motherboard was made, what was the difference between
the motherboards?
The original was obviously a Dell MBD, and what about the replacement?
It may be that the difference is not enough to cause major problems, just
minor ones, such as you have.
You did not mention what you did after you replaced the MBD. Did you
re-install windows? Or use the original install.
Remember that the original install may not be configured exactly properly
for the new MBD.
As to MBD options, they vary quite a bit from MBD to MBD. There may or may
not be a BIOS setting that makes a difference.
I'd likely try removing and reinstalling the USB subsystem drivers for the
controller and ports, just to test a faint hope that the problem might be
solved. It may also be that the original Dell MBD had some Dell specific
drivers that were not applicable to the new MBD.
If both MBDs are Dell MBDs, Dell might be a place to obtain information
specific to your new MBD & it's capabilities.